Here's a list from the back of a Chinese Foguang Shan edition of Linji Yulu.

It's hard to work out whether Linji was consciously quoting a specific text, or just using a phrase that was common in Buddhist discussion at the time. For example, the Sarvastivada vinaya 'quotation' seems to refer to the fact that Linji's description of the Five Heinous Crimes 'seems presaged' by the description in the Sarvastivada vinaya (i got this by searching for 'vinaya' in google books version of Ruth Sasaki's translation + notes. I can't easily find the sarvastivadavinaya-related footnote in my Chinese copy because it's paper with no index!) Likewise, the Agama references I can find through Sasaki's searchable Google Books copy are more influences rather than direct quotations.

Anyway, don't take this as a rock solid list, just an approximate impression. The list could be improved by including details of English translations, but I don't have time just now. In addition, I suppose one could try to find the quotations and put them under each text title, nicely set out in different coloured font! Even though this list is from a Taiwanese book, I think most of the quotations are findable by searching http://books.google.co.uk/books?id=Q_Je6UW0XxUC with the Chinese name of the text. I think Sasaki's book and my Taiwanese Foguang Shan copy both rely on the same Japanese scholars for the footnotes.

The numbers beginning T or X are Taishō or Zokuzokyo (Xuzangjing) sutra numbers.

Apparently the most quoted sutra in the Linji Yulu is the Vimalakirti Sutra, the most quoted Zen text is [Essentials on the Transmission of Mind-dharma/傳心法要], by [Huangbo Xiyun/Ōbaku Kiun].
For me the most interesting thing about the list is all those Zen poems (listed at the start of the 'Zen texts' section), most of which i'd never heard of. It's also interesting that Linji seems to have read or been influenced by a satipattana/mindfulness meditation sutra 正法念處經 (Saddharma)smṛtyupasthānasūtra (although at first glance it seems all he borrowed from that sutra was some striking imagery - King of Geese drinking milk from a bowl, dog licking a dry bone and mistaking his own saliva for juice).

Zen texts:一鉢歌 One Bowl Song梁寶誌和尚大乘讚十首 In Praise of Mahayana by the monk Liang Baozhi三祖僧璨大師信心銘 Faith in Mind Inscription by Third Patriarch Sengcan樂道歌 Song of Enjoying the Way, Nanyue Mingzan蘇溪和尚牧護歌 Song of the Herdsman by the monk Suxi丹霞和尚玩珠吟 Playing with the Pearl by the monk Danxia關南長老獲珠吟 Obtaining the Pearl by the Venerable Guannan譚道頌 Poem on Discussing the Dao, by Zhixian